P0: project setup (packaging, CI, licences, data/oracle scripts)

- pyproject (uv/hatch, ruff, mypy strict, pytest markers), MIT LICENSE,
  THIRD_PARTY_NOTICES with verbatim BSD-2 (BeadArrayFiles) and MIT (gtc2vcf)
- CI workflow for Gitea/GitHub Actions: lint, type check, unit tests
- fetch_data.sh p0 now fetches the GSA v4 PGx demo IDATs (the GDA "Demo 36"
  bundle is a GenomeStudio project), unpacks archives, fixes pipefail bug
- make_oracle_gtcs.sh builds bcftools + gtc2vcf and writes oracle GTCs
- plan §17: corrected P0 dataset table

README.md

@@ -3,10 +3,25 @@
 Personal research toolkit for Illumina Infinium genotyping BeadChip data
 (IDAT → normalization → genotype calling → BAF/LRR → QC → VCF/PLINK; later CN/LOH, PGx, cluster training).
 
-Start with **SIMURGARRAY_MASTER_PLAN.md** (architecture, algorithms, roadmap) and
-**SIMURGARRAY_FUNCTIONAL_SPEC.md** (416 itemised requirements: CLI, inputs, outputs, QC, CN, PGx, methylation, edge cases).
+- **SIMURGARRAY_MASTER_PLAN.md** — architecture, algorithms, roadmap
+- **SIMURGARRAY_FUNCTIONAL_SPEC.md** — 416 itemised requirements (CLI, inputs, outputs, QC, CN, PGx, methylation, edge cases)
+- `docs/validation/` — per-phase validation reports · `docs/known_unknowns.md` — findings log · `docs/research/` — background
+
+## Status
+
+Phases **P0 (setup)** and **P1 (file parsers)** are complete — see `docs/validation/P1.md`.
+Available commands: `simurg version`, `simurg inspect <files…> [--json]`.
+
+## Quick start
 
 ```bash
-bash scripts/bootstrap_refs.sh     # clone reference open-source repos into refs/
-bash scripts/fetch_data.sh p0      # download small test datasets into data/
+uv venv && uv pip install -e ".[dev]"
+uv run pytest tests/unit                  # no downloads needed
+bash scripts/bootstrap_refs.sh            # reference open-source repos → refs/ (oracles)
+bash scripts/fetch_data.sh p0             # ~1.4 GB of public test data → data/
+bash scripts/make_oracle_gtcs.sh          # builds gtc2vcf, writes oracle GTCs
+uv run pytest tests/oracle                # real-data acceptance tests (add -m "not slow" to skip the long ones)
+uv run simurg inspect data/p0/gsa_v4_pgx/idats_Demo_36/idats_Demo_36/207895980019/207895980019_R03C01_Grn.idat
 ```
+
+Vendor data files are downloaded for personal research use only and are never committed. See `THIRD_PARTY_NOTICES.md`.